CN File

What are CN files and how to open them

Are you having problems opening a CN file or are you simply curious about its contents? We're here to explain the properties of these files and provide you with software that can open or handle your CN files.

What is a CN file?

A .CN file is a Copy Numbers Format file.

Copy Numbers format stores raw copy number values for single-nucleotide polymorphism (SNP) probes across multiple SNP array samples in a plain text table. It is meant as input for GenePattern modules that analyze SNP copy numbers to detect genomic variation. Each row represents one SNP probe and each column (after the first few fixed columns) represents the numeric copy number measured in a particular sample.

GenePattern creates Copy Numbers files when converting SNP array data into copy number input for downstream modules. These files are used directly by modules that expect copy-number measurements rather than intensity or genotype calls. Workflows that segment, normalize, or compare copy number across samples typically take a CN file as input. CN files must be tab-delimited, with one header line listing fixed identifiers followed by array sample names, and one data row per SNP.

The first line of a CN file gives column headers in this order: SNP, Chromosome, PhysicalPosition, then one header per SNP array sample. Each subsequent line contains the SNP identifier, its chromosome, its physical position (genomic base pair coordinate), and the raw numeric copy number values for each sample. Sample columns are sorted and SNP rows should be ordered by chromosome and by increasing physical position.

Files in this format begin with the ASCII signature "SNP.Chromosome.PhysicalPosition" at byte offset 0.

How to open CN files

Important: Different programs may use files with the CN file extension for different purposes, so unless you are sure which format your CN file is, you may need to try a few different programs.

While we have not verified the app ourselves yet, our users have suggested a single CN opener which you will find listed below.

Last updated: August 31, 2026

Various apps that use files with this extension

These apps are known to open certain types of CN files. Remember, different programs may use CN files for different purposes, so you may need to try out a few of them to be able to open your specific file.

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